MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

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Processing Stage Template Semi-Empirical QM (QM0) DFT QM (QM1) DFT Hessian QM (QM2)
Calculation None Energy Minization Energy Minization Hessian
Level of Theory None Semi-Empirical / SCF DFT (B3LYP/6-31G*) DFT (B3LYP/6-31G*)
Default Size Limit (Atoms) 2000 500 50 40
Content of MD Topology
Charges Derived From None MOPAC Merz-Singh-Kollman Merz-Singh-Kollman
Geometry  User Provided Optimized Optimized Optimized
Non-Bonded Interactions Bonds Rule Based:

Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.

Hessian Based:

Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.

Angles
Dihedrals

Data

Current Processing StateCompleted
Total Processing TimeNA (hh:mm:ss)

Molecule Information

Molecule Typeamino acid building block
Residue Name (RNME)T2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge-2
Forcefieldmultiple
Molecule ID17346
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:16
Literature ReferenceDrazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

Topology History

Other conformers for this molecule (201-300 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation > Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17399 None - 21 0 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
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ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)